Aligments for a candidate for hisN in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Aligments for a candidate for hisN in Phaeobacter inhibens BS107

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate GFF2154 PGA1_c21860 putative histidinol-phosphate phosphatase HisN

Query= reanno::Phaeo:GFF2154
         (250 letters)



>lcl|FitnessBrowser__Phaeo:GFF2154 PGA1_c21860 putative
           histidinol-phosphate phosphatase HisN
          Length = 250

 Score =  495 bits (1275), Expect = e-145
 Identities = 250/250 (100%), Positives = 250/250 (100%)

Query: 1   MADAARQAILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILGEEF 60
           MADAARQAILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILGEEF
Sbjct: 1   MADAARQAILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILGEEF 60

Query: 61  GETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPE 120
           GETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPE
Sbjct: 61  GETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPE 120

Query: 121 GASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDCYA 180
           GASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDCYA
Sbjct: 121 GASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDCYA 180

Query: 181 YALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELHA 240
           YALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELHA
Sbjct: 181 YALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELHA 240

Query: 241 AALALIQQTA 250
           AALALIQQTA
Sbjct: 241 AALALIQQTA 250


Lambda     K      H
   0.317    0.134    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 345
Number of extensions: 7
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 250
Length of database: 250
Length adjustment: 24
Effective length of query: 226
Effective length of database: 226
Effective search space:    51076
Effective search space used:    51076
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate GFF2154 PGA1_c21860 (putative histidinol-phosphate phosphatase HisN)
to HMM TIGR02067 (hisN: histidinol-phosphatase (EC 3.1.3.15))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR02067.hmm
# target sequence database:        /tmp/gapView.32202.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02067  [M=252]
Accession:   TIGR02067
Description: his_9_HisN: histidinol-phosphatase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    2.1e-89  285.3   0.1    2.4e-89  285.1   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2154  PGA1_c21860 putative histidinol-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2154  PGA1_c21860 putative histidinol-phosphate phosphatase HisN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.1   0.1   2.4e-89   2.4e-89       8     251 ..       1     246 [.       1     247 [. 0.98

  Alignments for each domain:
  == domain 1  score: 285.1 bits;  conditional E-value: 2.4e-89
                          TIGR02067   8 laeaageailkyfrasdlkvdkksdk..tpVteADraaEeaireliaakfPddgilGEEfgeeeedaeyvWvlDPi 81 
                                        +a+aa++ail+yfr   l+ d+k d+  +pVt+ADraaE+a+r+++++ +P+d+ilGEEfge++++++++WvlDPi
  lcl|FitnessBrowser__Phaeo:GFF2154   1 MADAARQAILPYFRSAGLQSDNKLDEgfDPVTIADRAAEQAMRSVLSELRPEDSILGEEFGETHGQSGRTWVLDPI 76 
                                        69*********************9999************************************************* PP

                          TIGR02067  82 DGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallng.gerelrvsevaklsdAvlvttspk 156
                                        DGT+ Fi+G P wg+LiaL +++ p lG+++qP++gerf+++ ++++l+ + g++ l ++++ +ls+A+l+tt p 
  lcl|FitnessBrowser__Phaeo:GFF2154  77 DGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPEGASLTGPlGHSALVTRATDSLSEATLFTTFP- 151
                                        *************************************************99777*********************. PP

                          TIGR02067 157 aledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipiieeAggvitdwkGkeaeeg 232
                                        ++ +e+er+af+++ +++rltryg dcyayal+A+G+ dlv+ea+l++yDi+a i +i+ Aggv+t+w+G++a+eg
  lcl|FitnessBrowser__Phaeo:GFF2154 152 EVGTEAERAAFQRVSAQVRLTRYGMDCYAYALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEG 227
                                        7*************************************************************************** PP

                          TIGR02067 233 geavaaanaalhdevlell 251
                                        g+++aaa+a+lh+++l+l+
  lcl|FitnessBrowser__Phaeo:GFF2154 228 GQVLAAATAELHAAALALI 246
                                        ****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (252 nodes)
Target sequences:                          1  (250 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 6.93
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis